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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-phylogeny">Debian Med / q2-phylogeny</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-phylogeny/-/commit/6d15b55b93e7c397dc2cd25f9415ea9cb7589285">6d15b55b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-18T17:30:14+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/salsa-ci.yml: Do not run build on i386
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-phylogeny/-/commit/4a3a351f33008a43ba9109158cfebb44912ea1e9">4a3a351f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-18T18:34:44+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/patches/*: Fix tests, change binary names, options as available
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-phylogeny/-/commit/b051046877850e06be825be99c05e6490f5f0a8d">b0510468</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-18T18:35:04+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depends on q2-{alignment, types}
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-phylogeny/-/commit/52670b842d74f6968d49dde2455a67b152fdae46">52670b84</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-18T18:44:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: Do not circumvent tests with || true. Rather simply do not run them
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-phylogeny/-/commit/49930281c9f56d8711f61d403ba38e07231f3a4f">49930281</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-18T18:44:23+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: Drop un-necessary build-deps
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#00fa59d0c4c4aa6da60d5715d351f50ee6f2d619">
<span class="new-file">
+
debian/patches/fix-tests-and-binary-names-and-options.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
debian/salsa-ci.yml
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/q2-phylogeny/-/compare/8617cca56417ffdf5cacf1aaacb3b5bf93a442f2...49930281c9f56d8711f61d403ba38e07231f3a4f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,15 +6,7 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> python3-skbio,</span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python3-pytest-cov,</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> qiime,</span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> q2-types,</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> fasttree,</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> iqtree,</span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> mafft,</span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> raxml</span>
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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3-setuptools</span>
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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/q2-phylogeny</span>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
20
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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/q2-phylogeny.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,7 +24,9 @@ Depends: ${shlibs:Depends},</td>
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32
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24
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> fasttree,</span>
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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
33
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> iqtree,</span>
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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> mafft,</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> raxml</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> raxml,</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> q2-types,</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> q2-alignment</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Description: QIIME 2 plugin for phylogeny</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> QIIME 2 plugin for phylogenetic reconstruction, and operations on</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> phylogenetic trees.</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-phylogeny/-/compare/8617cca56417ffdf5cacf1aaacb3b5bf93a442f2...49930281c9f56d8711f61d403ba38e07231f3a4f#00fa59d0c4c4aa6da60d5715d351f50ee6f2d619"><strong>debian/patches/fix-tests-and-binary-names-and-options.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Following things:</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> - Renamed binaries according to the names available in our distribution</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> - Disabled one failing test</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> - Remove tests which test SSE or AVX extensions of raxml</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> - Modify a test to use Standard raxml rather than SSE3</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Last-Update: 2021-07-18</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/q2_phylogeny/tests/test_raxml.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/q2_phylogeny/tests/test_raxml.py</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -88,37 +88,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> self.assertTrue('raxmlHPC' in str(obs_stand_1[0]))</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> self.assertTrue(len(obs_stand_1) == 1)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_sse3_1 = _set_raxml_version(raxml_version='SSE3', n_threads=1)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('raxmlHPC-SSE3' in str(obs_sse3_1[0]))</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(len(obs_sse3_1) == 1)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_avx2_1 = _set_raxml_version(raxml_version='AVX2', n_threads=1)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('raxmlHPC-AVX2' in str(obs_avx2_1[0]))</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(len(obs_avx2_1) == 1)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_stand_4 = _set_raxml_version(raxml_version='Standard',</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- n_threads=4)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('raxmlHPC-PTHREADS' in str(obs_stand_4[0]))</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('4' in str(obs_stand_4[1]))</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(len(obs_stand_4) == 2)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_sse3_4 = _set_raxml_version(raxml_version='SSE3', n_threads=4)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('raxmlHPC-PTHREADS-SSE3' in str(obs_sse3_4[0]))</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('4' in str(obs_sse3_4[1]))</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(len(obs_sse3_4) == 2)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_avx2_4 = _set_raxml_version(raxml_version='AVX2', n_threads=4)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('raxmlHPC-PTHREADS-AVX2' in str(obs_avx2_4[0]))</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('4' in str(obs_avx2_4[1]))</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(len(obs_avx2_4) == 2)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> def test_raxml_version(self):</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> # Test that an output tree is made when invoking threads.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> with redirected_stdio(stderr=os.devnull):</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs = raxml(input_sequences, raxml_version='SSE3')</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ obs = raxml(input_sequences, raxml_version='Standard')</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> # load the resulting tree and test that it has the right number of</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/q2_phylogeny/_fasttree.py</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/q2_phylogeny/_fasttree.py</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -40,7 +40,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> env = os.environ.copy()</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> n_threads = 0 if n_threads == 'auto' else n_threads</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> env.update({'OMP_NUM_THREADS': str(n_threads)})</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd = ['FastTreeMP']</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = ['fasttreeMP']</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> cmd.extend(['-quote', '-nt', aligned_fp])</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> run_command(cmd, tree_fp, env=env)</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/q2_phylogeny/_iqtree.py</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/q2_phylogeny/_iqtree.py</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -75,7 +75,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> '-pre', str(run_prefix)]</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> if n_cores == 'auto' and n_cores_max:</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd += ['-nt', 'AUTO', '--threads-max', '%i' % n_cores_max]</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd += ['-nt', 'AUTO', '-ntmax', '%i' % n_cores_max]</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> elif n_cores == 'auto' and n_cores_max is None:</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> cmd += ['-nt', 'AUTO']</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> else:</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -217,7 +217,7 @@</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> '-pre', str(run_prefix)]</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> if n_cores == 'auto' and n_cores_max:</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd += ['-nt', 'AUTO', '--threads-max', '%i' % n_cores_max]</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd += ['-nt', 'AUTO', '-ntmax', '%i' % n_cores_max]</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> elif n_cores == 'auto' and n_cores_max is None:</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> cmd += ['-nt', 'AUTO']</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> else:</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/q2_phylogeny/tests/test_iqtree.py</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/q2_phylogeny/tests/test_iqtree.py</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -332,7 +332,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> exp_tree = skbio.TreeNode.read(self.get_data_path('test5.tre'))</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> exp_supp = [node.name for node in exp_tree.non_tips()]</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> </span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(set(obs_supp), set(exp_supp))</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> self.assertEqual(len(obs_supp[0].split('/')), 4) # should be 4 values</span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> self.assertEqual(len(exp_supp[0].split('/')), 4) # should be 4 values</span>
</pre>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/q2-phylogeny/-/compare/8617cca56417ffdf5cacf1aaacb3b5bf93a442f2...49930281c9f56d8711f61d403ba38e07231f3a4f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix-tests-and-binary-names-and-options.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-phylogeny/-/compare/8617cca56417ffdf5cacf1aaacb3b5bf93a442f2...49930281c9f56d8711f61d403ba38e07231f3a4f#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,9 +14,8 @@ export PYBUILD_BEFORE_INSTALL=rm -rvf {build_dir}/q2-phylogeny.egg-* {build_dir}</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">#FIXME: Delaying true testing to autopkgtests since QIIME2 module cannot be registered</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># at build time.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">#FIXME:</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <span class="idiff left right">dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_phylogeny" || true</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> <span class="idiff left right">echo "I: Delaying true testing to autopkgtests since QIIME2 module cannot be registered at build time"</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">endif</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-phylogeny/-/compare/8617cca56417ffdf5cacf1aaacb3b5bf93a442f2...49930281c9f56d8711f61d403ba38e07231f3a4f#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,3 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># i386 CI disabled due to unavailable python3-skbio for i386 architecture</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">variables</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">SALSA_CI_DISABLE_BUILD_PACKAGE_I386</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">true"</span></span></pre>
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